I have experienced similar problems with my modded career game. For me the launch pad kept reverting back to level 1 whenever I entered the VAB. If I upgraded the launch pad to level 3, it would actually jump up to level 4 when entering the VAB. There were probably similar problems with all the other buildings in KSP as well.
I found the problem to be the following component:
SETI-CustomBarnKit-Config (EXPERIMENTAL) (SETI-CustomBarnKit 0.9.1.0)
After uninstalling that mod everything worked fine, but I would like to keep using that mod so a fix would be nice.
